Fig. 5

TPR and FDR stratified by incompleteness of annotation. The circles indicate the performance of the different methods using the complete annotation catalog. The triangles indicate the performance achieved when the analysis was performed using an incomplete annotation catalog, where 20 % of the transcripts were excluded. The overall impact of the incompleteness of the annotation catalog is larger for the fruit fly simulation (left panel) than for the human simulation (right panel). This appears to be mainly due to the larger number of isoforms in the human transcriptome and the associated larger redundancy. Additional file 1: Figs. S16–S19 stratify the results further and provide additional insight